It looks like you are using v2 (SDK Tools). The current version is Sencha Cmd v3.0.0.190 (at this moment).

In Cmd v3, there is no longer the need for a JSB file to maintain. The documentation has also been updated. The closest to what you might need is http://docs.sencha.com/ext-js/4-1/#!/guide/command_app_single

You may be able to set up your JSP file to use the new compiler's page command which would make compiling your page down to use a single JS file very simple.

If you want more control over how the JS code is packaged, you can use the lower-level compiler commands.